Trends in Genetics
Genome AnalysisAlternative splicing of conserved exons is frequently species-specific in human and mouse
Section snippets
Computational identification of AS events in human and mouse
We used computational methods initially to identify and analyze different types of AS events, including cassette, alternative 5′–3′ and mutually exclusive exons in 2603 unique human and mouse ortholog pairs (see the supplementary material online for the methods used). These ortholog pairs were selected from an initial starting set of 11 738 on the basis of several criteria including their representation in sequence databases by comparable numbers of corresponding transcript sequences (
Frequencies of conserved and species-specific alternative exons in human and mouse
Next, we analyzed the features of human and mouse cassette alternative exons, the most common type of AS. By comparing the genomic exon structures and mRNA and EST sequences of orthologs in our data sets, we estimated the relative proportions of AS events that are conserved between human and mouse versus those that are species-specific. Species-specific AS events were differentiated into two types: (i) those that are represented by conserved exons (‘species-specific AS of conserved exons’); and
Validation of computationally detected species-specific AS of conserved exons
To test the accuracy of our computational detection method and estimated frequencies of ‘high confidence’ species-specific AS of conserved exons, we performed RT–PCR assays on ten examples each of the human and mouse-specific AS events identified by our scoring scheme (Figure 1c). To facilitate unbiased and direct comparisons, the 20 examples were randomly selected from the high confidence set, with the additional criterion that they are represented by human and mouse mRNAs and ESTs from the
Functional significance of species-specific AS of conserved exons
To what extent is species-specific AS of conserved exons likely to represent a process that is under evolutionary selection pressure and, therefore, of functional importance, as opposed to representing possible splicing errors? In the vast majority of the examples identified using our scoring scheme, exon skipping was detected in 5–95% of the mRNA and EST sequences sampled, and, in most cases, these examples were represented by sequences from more than one cell or tissue type. Thus, it is
Concluding remarks
We have provided evidence that at least 11% of human and mouse cassette AS events represent conserved exons that undergo species-specific AS. These species-specific AS events have the potential to modulate frequently the structural and functional properties of proteins that are attributed to conserved domains. Therefore, they could have an important role in the evolutionary differences between mammalian species. Future experimental studies will be required to determine the precise contribution
Update
While this article was in preparation, the authors confirmed experimentally the differences in global inclusion-level properties of conserved and species-specific alternative exons shown in Figure 2a, using a new quantitative AS microarray profiling system [10].
Acknowledgements
We thank Jim Friesen, Alan Cochrane and members of the Blencowe Laboratory for their helpful comments on this article. This work was supported by an operating grant from the CIHR to B.J.B.
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